We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.

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The SIESTA method for ab initio order-N materials simulation

In this work we briefly describe the most relevant features of WSXM, a freeware scanning probe microscopy software based on MS-Windows. The article is structured in three different sections: The introduction is a perspective on the importance of software on scanning probe microscopy. The second section is devoted to describe the general structure of the application; in this section the capabilities of WSXM to read third party files are stressed. Finally, a detailed discussion of some relevant procedures of the software is carried out.

https://nanoed.tul.cz/pluginfile.php/1608/mod_resource/content/1/view.pdf

WSXM: a software for scanning probe microscopy and a tool for nanotechnology.

/pdf/honeycomb-carbon-a-review-of-graphene-bjl5wl6ai8.pdf

Honeycomb Carbon: A Review of Graphene

We introduce the 2D counterpart of layered black phosphorus, which we call phosphorene, as an unexplored p-type semiconducting material. Same as graphene and MoS2, single-layer phosphorene is flexible and can be mechanically exfoliated. We find phosphorene to be stable and, unlike graphene, to have an inherent, direct, and appreciable band gap. Our ab initio calculations indicate that the band gap is direct, depends on the number of layers and the in-layer strain, and is significantly larger than the bulk value of 0.31–0.36 eV. The observed photoluminescence peak of single-layer phosphorene in the visible optical range confirms that the band gap is larger than that of the bulk system. Our transport studies indicate a hole mobility that reflects the structural anisotropy of phosphorene and complements n-type MoS2. At room temperature, our few-layer phosphorene field-effect transistors with 1.0 μm channel length display a high on-current of 194 mA/mm, a high hole field-effect mobility of 286 cm2/V·s, and an...

/pdf/phosphorene-an-unexplored-2d-semiconductor-with-a-high-hole-pehm34p0g2.pdf

Phosphorene: An Unexplored 2D Semiconductor with a High Hole Mobility

https://www.zora.uzh.ch/id/eprint/3175/3/PP_VandeVondele_CPCom_2005QuickManVO.pdf

QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach

The properties of small clusters Fe 3 and Fe 5 , in which the non-collinearity of magnetic density is expected to be important, and of larger nanoparticles (consisting of up to 62 atoms) are studied from first principles making use of density functional theory, norm-conserving pseudopotential and numerical local orbitals method, as implemented in the SIESTA code. We concentrate on the interplay of lattice relaxation, mostly pronounced near the surface of particles, and the particles' magnetic characteristics. Previously obtained theoretical findings of enhanced magnetic moments in outer shells of nanoparticles are confirmed. These results are refined by taking structure relaxation into account and by considering more representative bcc- and fcc-related particles; moreover, we allowed antiferromagnetic ordering along with ferromagnetic one.

First-Principles Simulations of Atomic Structure and Magnetism in Fe Nanoparticles

We have applied first-principles density-functional calculations to the study of the energetics, and the elastic and electronic properties of monatomic wires of Au, Cu, K, and Ca in linear and a planar-zigzag geometries. 
For Cu and Au wires, the zigzag distortion is favorable even when the linear wire is stretched, but this is not observed for K and Ca wires. 
In all the cases, the equilibrium structure is an equilateral zigzag (bond angle of 60$^{\rm o}$). 
Only in the case of Au, the zigzag geometry can also be stabilized for an intermediate bond angle of 131$^{\rm o}$. 
The relationship between the bond and wire lengths is qualitatively different for the metallic (Au, Cu and, K) and semiconducting (Ca) wires.

Zigzag equilibrium structure in monatomic wires

In this work we address the behaviour of electronic structure under uniaxial stress, by first-principles calculations and experiments of conductance in nanometer-sized metallic contactes of Au and Al. These contacts are shown to be specially suitable for this purpose. The conductance behaviour is related to the change with strain of Fermi surface. Both experimental and theoretically Au behaves like the free electron gas but Al has the opposite behaviour.

Electronic Structure Under Extreme Uniaxial Strains: Conductance in Metallic Nanocontacts

The presence of sharp peaks in the real part of the static dielectric response function are usually accepted as indication of charge or spin instabilities in a material. However, there are misconceptions that Fermi surface (FS) nesting guarantees a peak in the response function like in one-dimensional systems, and, in addition, response function matrix elements between empty and occupied states are usually considered of secondary importance and typically set to unity like in the free electron gas case. In this work, we explicitly show, through model systems and real materials, within the framework of density functional theory, that predictions about the peaks in the response function, using FS nesting and constant matrix elements yields erroneous conclusions. We find that the inclusion of the matrix elements completely alters the structure of the response function. In all the cases studied other than the one-dimensional case we find that the inclusion of matrix elements washes out the structure found with constant matrix elements. Our conclusion is that it is imperative to calculate the full response function, with matrix elements, when making predictions about instabilities in novel materials.

Critical analysis of the response function in low-dimensional materials.

We present a simple view on band unfolding of the energy bands obtained from supercell calculations. It relies on the relationship between the local density of states in reciprocal space (qLDOS) and the fully unfolded band structure. This provides an intuitive and valid approach not only for periodic, but also for systems with no translational symmetry. By refolding into the primitive Brillouin zone of the pristine crystal we recover the conventional unfolded bands. We implement our algorithm in the SIESTA package and apply it to defects on Si and graphene.

José M. Soler

Papers

First-Principles Simulations of Atomic Structure and Magnetism in Fe Nanoparticles

Zigzag equilibrium structure in monatomic wires

Electronic Structure Under Extreme Uniaxial Strains: Conductance in Metallic Nanocontacts

Critical analysis of the response function in low-dimensional materials.

Band Unfolding Made Simple